LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -61.041289 0.0000000) to (24.920002 61.041289 8.6325418) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9808004 5.2902450 5.7550279 Created 1193 atoms using lattice units in orthogonal box = (0.0000000 -61.041289 0.0000000) to (24.920002 61.041289 8.6325418) create_atoms CPU = 0.005 seconds 1193 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9808004 5.2902450 5.7550279 Created 1201 atoms using lattice units in orthogonal box = (0.0000000 -61.041289 0.0000000) to (24.920002 61.041289 8.6325418) create_atoms CPU = 0.005 seconds 1201 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 39 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 2385 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_769632475533_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.576 | 5.576 | 5.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10172.132 0 -10172.132 55086.557 79 0 -10605.757 0 -10605.757 884.33256 Loop time of 3.11657 on 1 procs for 79 steps with 2385 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10172.132187178 -10605.7476568198 -10605.756659914 Force two-norm initial, final = 712.65737 0.40722496 Force max component initial, final = 115.67042 0.14682836 Final line search alpha, max atom move = 1.0000000 0.14682836 Iterations, force evaluations = 79 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9769 | 2.9769 | 2.9769 | 0.0 | 95.52 Neigh | 0.078388 | 0.078388 | 0.078388 | 0.0 | 2.52 Comm | 0.026369 | 0.026369 | 0.026369 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03489 | | | 1.12 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7501.00 ave 7501 max 7501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204664.0 ave 204664 max 204664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204664 Ave neighs/atom = 85.812998 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.576 | 5.576 | 5.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -10605.757 0 -10605.757 884.33256 26262.765 81 0 -10605.791 0 -10605.791 -9.9179069 26274.655 Loop time of 0.112516 on 1 procs for 2 steps with 2385 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10605.756659914 -10605.7852526057 -10605.7905257728 Force two-norm initial, final = 53.173719 1.0685885 Force max component initial, final = 45.748908 0.92655873 Final line search alpha, max atom move = 3.5786283e-05 3.3158093e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10827 | 0.10827 | 0.10827 | 0.0 | 96.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083236 | 0.00083236 | 0.00083236 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003413 | | | 3.03 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7503.00 ave 7503 max 7503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204648.0 ave 204648 max 204648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204648 Ave neighs/atom = 85.806289 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.714 | 5.714 | 5.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10605.791 0 -10605.791 -9.9179069 Loop time of 6.405e-06 on 1 procs for 0 steps with 2385 atoms 203.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.405e-06 | | |100.00 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7503.00 ave 7503 max 7503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204634.0 ave 204634 max 204634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204634 Ave neighs/atom = 85.800419 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.714 | 5.714 | 5.714 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -10605.791 -10605.791 24.925895 122.20841 8.6255181 -9.9179069 -9.9179069 -56.513079 19.031308 7.7280503 2.2156933 671.45216 Loop time of 6.866e-06 on 1 procs for 0 steps with 2385 atoms 247.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.866e-06 | | |100.00 Nlocal: 2385.00 ave 2385 max 2385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7503.00 ave 7503 max 7503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102317.0 ave 102317 max 102317 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204634.0 ave 204634 max 204634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204634 Ave neighs/atom = 85.800419 Neighbor list builds = 0 Dangerous builds = 0 2385 -10605.7905257728 eV 2.21569330167221 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04